Re: [galaxy-dev] Galaxy Slurm job_conf.xml

[Sven E Templer]

Hi Simon,

we use slurm via drmaa. Find configurations here:

https://github.com/mpg-age-bioinformatics/galaxy-admin/tree/master/server/config
https://github.com/mpg-age-bioinformatics/galaxy-admin/tree/master/system

Best,
Sven

> On 15 Oct 2015, at 08:38, Björn Grüning  wrote:
> 
> Hi Simon,
> 
> the Galaxy Docker Image is using Slurm you can look at it here:
> 
> https://github.com/bgruening/docker-galaxy-stable
> 
> Hope this helps,
> Bjoern
> 
> Am 15.10.2015 um 06:38 schrieb Simon Gladman:
>> Hi there all,
>> 
>> Has anyone had success setting up job_conf.xml for slurm based clusters? I
>> am having trouble getting the GALAXY_SLOTS env var set for any jobs. I've
>> tried looking at destinations in the job_conf.xml but can't get
>> SLURM_NTASKS to be set correctly so the slurm run script can translate that
>> into GALAXY_SLOTS..
>> 
>> Does anyone have a toy example of a job_conf.xml for slurm that they
>> wouldn't mind sharing?
>> 
>> Cheers,
>> 
>> Simon.
>> 
>> 
>> 
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[galaxy-dev] Galaxy Slurm job_conf.xml

[Simon Gladman]

Hi there all,

Has anyone had success setting up job_conf.xml for slurm based clusters? I
am having trouble getting the GALAXY_SLOTS env var set for any jobs. I've
tried looking at destinations in the job_conf.xml but can't get
SLURM_NTASKS to be set correctly so the slurm run script can translate that
into GALAXY_SLOTS..

Does anyone have a toy example of a job_conf.xml for slurm that they
wouldn't mind sharing?

Cheers,

Simon.

-- 
Simon Gladman | Bioinformatician
Victorian Life Sciences Computation Initiative - LSCC
700 Swanston Street, The University of Melbourne | Victoria 3010 Australia
T +61 3 9035 5822 | M 0418 421 077
Mail: simon.glad...@unimelb.edu.au
Web: http://www.vlsci.org.au
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